rs12580100

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.145 in 152,086 control chromosomes in the GnomAD database, including 1,869 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.15 ( 1869 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.431
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.145
AC:
22072
AN:
151966
Hom.:
1867
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.113
Gnomad AMI
AF:
0.127
Gnomad AMR
AF:
0.199
Gnomad ASJ
AF:
0.117
Gnomad EAS
AF:
0.229
Gnomad SAS
AF:
0.338
Gnomad FIN
AF:
0.155
Gnomad MID
AF:
0.146
Gnomad NFE
AF:
0.133
Gnomad OTH
AF:
0.143
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.145
AC:
22089
AN:
152086
Hom.:
1869
Cov.:
31
AF XY:
0.151
AC XY:
11210
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.113
Gnomad4 AMR
AF:
0.199
Gnomad4 ASJ
AF:
0.117
Gnomad4 EAS
AF:
0.229
Gnomad4 SAS
AF:
0.336
Gnomad4 FIN
AF:
0.155
Gnomad4 NFE
AF:
0.133
Gnomad4 OTH
AF:
0.148
Alfa
AF:
0.138
Hom.:
3371
Bravo
AF:
0.142
Asia WGS
AF:
0.310
AC:
1077
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.2
DANN
Benign
0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12580100; hg19: chr12-56439209; API